/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb is in gromacs-data 4.5.5-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 | [ None ]
[ GLY-NH3+ ]
[ replace ]
N N NH3 14.0027 -0.3
CA CA CT2 12.011 0.13
[ Add ]
3 4 H N CA C
HC 1.008 0.33 -1
[ delete ]
HN
[ NH3+ ]
[ replace ]
N N NH3 14.0027 -0.3
CA CA CT1 12.011 0.21
HA HA HB 1.008 0.10
[ Add ]
3 4 H N CA C
HC 1.008 0.33 -1
[ delete ]
HN
[ PRO-NH2+ ]
[ replace ]
N N NP 14.0027 -0.07
CA CA CP1 12.011 0.16
CD CD CP3 12.011 0.16
[ add ]
2 4 H N CA C
HC 1.008 0.24 -1
;
[ NH2 ]
[ replace ]
N NH2 14.0067 -0.96
CA CT1 12.011 0.19
HA HB 1.008 0.09
[ add ]
2 4 HT N CA C
H 1.008 0.34 -1
[ delete ]
HN
;
[ GLY-NH2 ]
[ replace ]
N NH2 14.0067 -0.96
CA CT2 12.011 0.10
[ add ]
2 4 HT N CA C
H 1.008 0.34 -1
[ delete ]
HN
;
[ PRO-NH ]
[ replace ]
N NP 14.0027 -0.40
CA CP1 12.011 -0.08
CD CP3 12.011 -0.10
[ add ]
1 4 H N CA C
HC 1.008 0.31 -1
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